EGAD Library Manual

Table of Contents

  1. Introduction
    1. Welcome
    2. Using This Manual
    3. Installation
    4. Library Structure
  2. Physical Models
    1. Rotamers and the Fixed Backbone
    2. Atom and Residue Data
    3. Proteins
  3. Energy Functions
    1. Vacuum Energies
    2. Solvation Effects
    3. Preparing for Minimization
  4. Minimizers
    1. Deterministic Algorithms
    2. Stochastic Algorithms
  5. Utilities
    1. Error Checking
  6. Advanced Techniques
    1. Polymers of Macromolecules
    2. Ligands
    3. Multiple States
  7. Appendix
    1. Class Documentation
    2. File Formats